Running MirMark Code

Run the test example by executing the code:

# Fetch the example files
cd ~
wget http://mn.eng.hawaii.edu/~garmire/MirMarkTest.tgz
tar zxvf MirMarkTest.tgz
cd MirMarkTest
# docker needs to connect the directory "MirMarkTest" to the Docker image
# It does this through the "-v {host directory:image directory}" option.
# The -w option establishes the working directory.
# All other mirmark perl scripts can be run in the same manner.
siteFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt site_features rf.site.model
# The result is stored in MirMarkTest/site_features.result
utrFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt utr_features rf.utr.model
# The result is stored in MirMarkTest/utr_features.result

Docker installation

Docker is another method of running code on a different OS like Windows
or Mac. It works by running a virtual machine through VirtualBox. The list
of commands below should work once Docker is installed.

Pull MirMark Image

The MirMark image should already be configured through the following Dockerfile. You should be able to pull this image by running in Docker: [docker pull dgarmire/mirmark]. You should be able to build this image by running [mkdir mirmark && wget http://mn.eng.hawaii.edu/~garmire/HTML/MirMark/Dockerfile && docker build -t dgarmire/mirmark .].

Running MirMark Code

To run the site and utr feature analysis using the example files provided:

# Fetch the example files
cd ~
wget http://mn.eng.hawaii.edu/~garmire/MirMarkTest.tgz
tar zxvf MirMarkTest.tgz
cd MirMarkTest
# docker needs to connect the directory "MirMarkTest" to the Docker image
# It does this through the "-v {host directory:image directory}" option.
# The -w option establishes the working directory.
# All other mirmark perl scripts can be run in the same manner.
docker run -w /tmp/mnt -v /home/docker/MirMarkTest:/tmp/mnt -t dgarmire/mirmark siteFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt site_features rf.site.model
# The result is stored in MirMarkTest/site_features.result
docker run -w /tmp/mnt -v /home/docker/MirMarkTest:/tmp/mnt -t dgarmire/mirmark utrFeaturesARFF.pl mirs.fa utrs.fa fast.txt pairs.txt utr_features rf.utr.model
# The result is stored in MirMarkTest/utr_features.result